Variant report

Variant	rs358708
Chromosome Location	chr3:155420726-155420727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155099990..155100742-chr3:155420395..155421265,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1005736	0.82[JPT][hapmap]
rs10936013	0.82[JPT][hapmap]
rs12486000	0.85[JPT][hapmap]
rs12488087	0.82[JPT][hapmap]
rs12490748	0.82[JPT][hapmap]
rs13076587	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13079863	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs13082287	0.82[JPT][hapmap]
rs13084995	0.86[ASN][1000 genomes]
rs13089059	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1519533	0.82[JPT][hapmap]
rs1519534	0.82[JPT][hapmap]
rs1519535	0.82[JPT][hapmap]
rs16825324	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs168601	0.81[JPT][hapmap]
rs1835212	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1879090	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1879091	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1879092	0.85[ASN][1000 genomes]
rs2222275	0.90[JPT][hapmap]
rs2435194	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2680881	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2680882	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34810038	0.84[ASN][1000 genomes]
rs358704	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs358706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358709	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358710	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358711	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358712	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs358727	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs358896	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358897	0.80[ASN][1000 genomes]
rs358898	0.86[ASN][1000 genomes]
rs358899	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358902	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358903	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs358905	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs358906	0.80[ASN][1000 genomes]
rs358910	0.86[ASN][1000 genomes]
rs358911	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358912	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs358913	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs359546	0.82[JPT][hapmap]
rs359560	0.82[JPT][hapmap]
rs359567	0.82[JPT][hapmap]
rs370157	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs378905	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs384412	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs386867	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs387885	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs392521	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs393081	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs394419	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs394440	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs397231	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs402201	0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs407212	0.98[ASN][1000 genomes]
rs407217	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4083041	0.86[ASN][1000 genomes]
rs412002	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs412664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs414126	0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs417877	0.88[ASN][1000 genomes]
rs421072	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs426069	0.99[ASN][1000 genomes]
rs429143	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs430008	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs446716	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs447359	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs447751	0.91[AMR][1000 genomes]
rs448062	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs498378	0.81[JPT][hapmap]
rs6441006	0.86[ASN][1000 genomes]
rs6772682	0.82[JPT][hapmap]
rs6777741	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6808257	0.82[JPT][hapmap]
rs7428196	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644902	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7645831	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155399800-155422000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:155400600-155421000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:155409200-155422200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:155412600-155422400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:155412600-155437400	Weak transcription	Pancreas	Pancrea
6	chr3:155413800-155432000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:155415000-155421200	Weak transcription	Stomach Mucosa	stomach
8	chr3:155415600-155421400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:155417400-155421600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:155418000-155421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:155418600-155421200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:155418800-155423400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:155418800-155423400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:155419200-155423600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:155419400-155421400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:155419600-155420800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:155419600-155422400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:155419800-155421200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:155419800-155421200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:155419800-155421200	Weak transcription	Brain Angular Gyrus	brain
21	chr3:155420000-155423800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:155420200-155421200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:155420200-155421200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:155420200-155421400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:155420200-155421600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:155420200-155421600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:155420200-155422200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:155420200-155422400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:155420200-155422600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:155420200-155422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:155420200-155432200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:155420400-155421600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:155420400-155422400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:155420600-155420800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:155420600-155421600	Enhancers	Fetal Intestine Large	intestine
36	chr3:155420600-155423000	Enhancers	Brain Germinal Matrix	brain

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